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Phylogeny

Phylogeny

Phylogeny is the inferred evolutionary history of a group of organisms (including microorganisms ). Paleontologists are interested in understanding life through time, not just at one time in the past or present, but over long periods of past time. Before they can attempt to reconstruct the forms, functions, and lives of once-living organisms, paleontologists have to place these organisms in context. The relationships of those organisms to each other are based on the ways they have branched out, or diverged, from a common ancestor. A phylogeny is usually represented as a phylogenetic tree or cladogram, which are like genealogies of species.

Phylogenetics, the science of phylogeny, is one part of the larger field of systematics, which also includes taxonomy. Taxonomy is the science of naming and classifying the diversity of organisms. Not only is phylogeny important for understanding paleontology (study of fossils), however, paleontology in turn contributes to phylogeny. Many groups of organisms are now extinct, and without their fossils we would not have as clear a picture of how modern life is interrelated.

There is an amazing diversity of life, both living and extinct. For scientists to communicate with each other about these many organisms, there must also be a classification of these organisms into groups. Ideally, the classification should be based on the evolutionary history of life, such that it predicts properties of newly discovered or poorly known organisms.

Phylogenetic systematics is an attempt to understand the evolutionary interrelationships of living things, trying to interpret the way in which life has diversified and changed over time. While classification is primarily the creation of names for groups, systematics goes beyond this to elucidate new theories of the mechanisms of evolution .

Cladistics is a particular method of hypothesizing relationships among organisms. Like other methods, it has its own set of assumptions, procedures, and limitations. Cladistics is now accepted as the best method available for phylogenetic analysis, for it provides an explicit and testable hypothesis of organismal relationships.

The basic idea behind cladistics is that members of a group share a common evolutionary history, and are "closely related," more so to members of the same group than to other organisms. These groups are recognized by sharing unique features that were not present in distant ancestors. These shared derived characteristics are called synapomorphies. Synapomorphies are the basis for cladistics.

In a cladistic analysis, one attempts to identify which organisms belong together in groups, or clades, by examining specific derived features or characters that those organisms share. For example, if a genus of bacteria forms a specific color or shaped colony , then those characters might be a useful character for determining the evolutionary relationships of other bacteria. Characters that define a clade are called synapomorphies. Characters that do not unite a clade because they are primitive are called plesiomorphies.

In a cladistic analysis, it is important to know which character states are primitive and which are derived (that is, evolved from the primitive state). A technique called outgroup comparison is commonly used to make this determination. In outgroup comparison, the individuals of interest (the ingroup) are compared with a close relative. If some of the individuals of the ingroup possess the same character state as the outgroup, then that character state is assumed to be primitive.

There are three basic assumptions in cladistics:

  1. Any group of organisms are related by descent from a common ancestor.
  2. There is a bifurcating pattern of cladogenesis.
  3. Change in characteristics occurs in lineages over time.

The first assumption is a general assumption made for all evolutionary biology. It essentially means that life arose on Earth only once, and therefore all organisms are related in one way or another. Because of this, scientists can take any collection of organisms and determine a meaningful pattern of relationships, provided they have the right kind of information.

The second assumption is that new kinds of organisms may arise when existing species or populations divide into exactly two groups. The final assumption, that characteristics of organisms change over time, is the most important assumption in cladistics. It is only when characteristics change that different lineages or groups are recognized. The convention is to call the "original" state of the characteristic plesiomorphic and the "changed" state apomorphic. The terms primitive and derived have also been used for these states, but they are often avoided by cladists, since those terms have been abused in the past.

Cladistics is useful for creating systems of classification. It is now the most commonly used method to classify organisms because it recognizes and employs evolutionary theory. Cladistics predicts the properties of organisms. It produces hypotheses about the relationships of organisms in a way that makes it possible to predict properties of the organisms. This can be especially important in cases when particular genes or biological compounds are being sought. Such genes and compounds are being sought all the time by companies interested in improving bacterial strains, disease resistance, and in the search for medicines. Only an hypothesis based on evolutionary theory, such as cladistic hypotheses, can be used for these endeavors.

As an example, consider the plant species Taxus brevifolia. This species produces a compound, taxol, which is useful for treating cancer. Unfortunately, large quantities of bark from this rare tree are required to produce enough taxol for a single patient. Through cladistic analysis, a phylogeny for the genus Taxus has been produced that shows Taxus cuspidata, a common ornamental shrub, to be a very close relative of T. brevifolia. Taxus cuspidata, then, may also produce large enough quantities of taxol to be useful. Having a classification based on evolutionary descent will allow scientists to select the species most likely to produce taxol.

Cladistics helps to elucidate mechanisms of evolution. Unlike previous systems of analyzing relationships, cladistics is explicitly evolutionary. Because of this, it is possible to examine the way characters change within groups over time, the direction in which characters change, and the relative frequency with which they change. It is also possible to compare the descendants of a single ancestor and observe patterns of origin and extinction in these groups, or to look at relative size and diversity of the groups. Perhaps the most important feature of cladistics is its use in testing long-standing hypotheses about adaptation.

See also Bacterial kingdoms; Evolution and evolutionary mechanisms; Evolutionary origin of bacteria and viruses; Microbial genetics; Viral genetics

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Phylogeny

Phylogeny

Before the mid-1800s, classification of organisms into groups, called taxa , was generally based on overall similarity of physical appearance. There was no guiding principle as to why the members of one group were more similar to each other than to the members of other groups. In 1859, Charles Darwin's Origin of Species was published, and Darwin's theory of evolution provided the explanation that natural groups occur because the members of the group are the descendants of a common ancestor. Based on Darwin's principles, in 1866, the German naturalist, Ernst Haeckel, coined the term phylogeny to describe the "science of the changes in form through which the phyla or organic lineages pass through the entire time of their discrete existence." Today the term phylogeny is used more widely to mean the evolutionary history or exact genealogy of a species or group of organisms. Phylogenies are based on the study of fossils, morphology, comparative anatomy, ultrastructure, biochemistry, and molecules.

Theoretical Foundations

In his explicit phylogenetic scheme for land plants, Haeckel rejected theories of multiple origins for organisms, which he called polyphyletic. He used the term monophyly to describe a natural group of two or more taxa whose members are all descended from the nearest common ancestor. Phylogenies are based on monophyletic groups. The taxonomic theory of phylogenetic systematics is organized around the principles that organisms are related through descent from a common ancestor, that there are natural groups of monophyletic taxa, and that unique changes or modifications shared by members of a taxon are evidence of their evolutionary history.

Although monophyletic taxa exist in nature whether they are discovered or not, the goal of phylogenetic systematics is to reveal natural groups of taxa. The main principle of phylogenetic systematics is that natural groups are defined by uniquely shared evolutionary novelties, or homologous characters. A character is a heritable feature (one that is passed from an ancestor to its descendants) of an organism that can be described, measured, or otherwise compared to other organisms. To be considered homologous, a character must be not only heritable, but also independent from any other characters in an organism. The different forms a character may take are called the character states.

Similarities and Phenetic Systems

Systems of classification that are based on overall similarity are called phenetic systems. Phenetic classification schemes do not distinguish between homologous characters (where taxa share a similar characteristic because they inherited it from a common ancestor) and analogous characters (where the characteristic shared by taxa was not inherited from a common ancestor). Sharing of homologous characters is evidence that taxa are evolutionarily related. For instance, the phloem that is found in carnations, roses, and lilies is a homologous similarity because all of these plants inherited the character from a common ancestor. The analogous phloemlike conducting tissue found in the giant kelps off the coast of California is functionally similar to phloem, but not inherited from the same common ancestor as the flowering plants. The evolution of analogous characters is also known as convergence or homoplasy, and often is the result of similar selection pressures in the environment on different organisms. In phylogenetic analysis, characters that are not recognized as being analogous can lead to unreliable results.

A homologous character can be an ancient retained feature, known as a plesiomorphy; while a homologous character that is the result of more recent evolutionary modifications is termed a derived character, or apomorphy. If taxa have the same apomorphy (that is, they share the same derived character), the character is termed a synapomorphy. German entomologist Willi Hennig, whose work was first translated into English in 1966, argued that only these shared, derived homologous characters (synapomorphies) could provide information about phylogeny, the evolutionary relationships of organisms. The methodology Hennig proposed to group taxa that share derived characters is now called cladistics.

The Rise of Cladistics

Cladistic analysis is designed to find evidence about which two taxa are more closely related to each other than either is to a third. Finding this evidence requires distinguishing between primitive and derived states of a character, a process known as determining character polarity. The most widely used method for determining character polarity is the outgroup method.

The outgroup method is comparative. If a group of organisms being compared (the in-group) shares a character state with organisms outside the group (the outgroup), then the character state is considered to be plesiomorphic, and this character provides no information about relationships among the in-group taxa. For instance, as in the example above, phloem is found in carnations, roses, and lilies (the in-group). Phloem is also found, however, in pine trees (the outgroup), and, therefore, in this instance the presence of phloem is plesiomorphic. These comparisons are also relative. The presence of phloem is considered apomorphic (and informative) when used as evidence of monophyly in higher plants, because although phloem is found in all higher green plants, it is not found in the lower green plants, such as green algae or bryophytes.

In cladistics, these hierarchical relationships are shown on a branching diagram that is called a cladogram (sometimes referred to as an evolutionary tree). Taxa that share many homologues will group together more closely on a cladogram than taxa that do not. All of the taxa on each branch of a cladogram are considered to form a monophyletic group, comprising of all the descendants of a common ancestor plus that ancestor. This group is also known as a clade. Clades that are next to each other on a cladogram are known as sister clades and the taxa in the clades as sister taxa.

Cladistic methodology is based on a type of logical reasoning called parsimony. The principle of parsimony states that of two hypotheses, the one that explains the data in the simplest manner, or with the smallest number of steps, is best. Looking again at the example of presence of phloem, the hypothesis that carnations, roses, and lilies all have phloem because they inherited it from a single common ancestor requires fewer evolutionary steps and is therefore more parsimonious than the hypothesis that phloem arose two or three separate times.

Phylogeny of the Green Plants

The concepts and practices discussed above have been used to study the phylogeny of the green plants as a whole, as well as many smaller groups of taxa. Although the presence of chlorophylls a and b was long thought to be a unifying character (synapomorphy) for the green plants, the fascinating phenomenon of endosymbiosis has resulted in organisms that are not green plants yet still have chlorophylls a and b. Specifically, the euglenophytes and the chloroarachniophytes, groups once considered to be green algae, carry the remains (that is, the chloroplasts) of their green algal endosymbionts, yet are themselves in very different evolutionary lineages than green algae.

For the true green algae and land plants, the whole array of characters mentioned earlier (for example, morphology, biochemistry, anatomy, and molecular comparisons) have provided some clear understanding of the basic phylogeny for this all-important groupthe green plantsupon which life depends.

One of the most interesting observations provided by current phylogenies is the fact that there are two major lineages of green photosynthetic organisms: the Chlorophyta, which includes only freshwater and marine green algae, and the Streptophyta, which includes some freshwater green algae and all of the land plants. Another interesting aspect of the phylogeny of green plants is that there was a single origin of the land plants from a green algal ancestor. Botanists are not absolutely certain which of the algae living today are the most closely related to the land plants, but they have narrowed the field to two groups.

Phylogenetic studies have also robustly established that the bryophytes (the mosses, liverworts, and hornworts) are the most primitive land plants. But, interestingly, there is still some uncertainly about which type of bryophyte is most closely related to the green algaethe hornworts or liverworts.

For the green plants, the phylogenetic history is not completely resolved, and scientists will continue using various methods of phylogenetic investigation to constantly improve and refine the understanding of the exact evolutionary history of all green plants, that is, the true phylogeny.

see also Darwin, Charles; Endosymbiosis; Evolution of Plants; Systematics, Molecular; Systematics, Plant; Taxonomy.

Russell L. Chapman

Debra A. Waters

Bibliography

Forey, P. L., C. J. Humphries, I. L. Kitching, R. W. Scotland, D. J. Siebert, and D. M. Williams. Cladistics: A Practical Course in Systematics. New York: Oxford University Press, 1994.

Hennig, Willi. Phylogenetic Systematics. Urbana, IL: University of Illinois Press, 1966.

Lipscomb, Diana. Basics of Cladistic Analysis. Washington, DC: George Washington University, 1998.

Raven, Peter H., Ray F. Evert, and Susan E. Eichhorn, eds. Biology of Plants, 6th ed. New York: W. H. Freeman and Company, 1999.

Strickberger, Monroe W. Evolution. Boston: Jones and Bartlett Publishers, 2000.

Wiley, E. O. Phylogenetics: The Theory and Practice of Phylogenetic Systematics, 3rd ed. New York: Wiley-Interscience, 1981.

"PRIMITIVE" VS. "ADVANCED" CHARACTERS

Fossil evidence has shown that bryophytes are the most primitive of the extant land plants. Bryophytes lack true xylem and phloem, although some mosses and liverworts have conducting tissues. Therefore, the absence of true xylem and phloem is a primitive feature. The presence of well-developed vascular tissue (xylem and phloem) in gymnosperms and angiosperms is a derived character.

Similarly, gymnosperms lack vessels in the xylem and angiosperms have vessels. The fossil record tells us that the gymnosperms came first, therefore, we know the vessels are a more recent, or derived, character. Often it is the fossil record that helps scientists polarize characters. For those plants for which we do not have an adequate fossil record, such as many of the green algae, polarizing characters and constructing a phylogeny becomes more difficult.

CHARACTER STATES

A botanist working with a particular group of flowering plants could observe that the flowers on some plants are red, whereas those on other plants are pink or white. The botanist might choose flower color as a character, with red, white, and pink as the character states.

If a character remains the same over generations with no changes, it will have only one state:

PinkPinkPinkPinkPink

However, if the character changes in a species and the change is transmitted to descendants, there will be more than one character state:

PinkWhiteWhiteWhite\RedRedRed

Choice of characters is one of the most important aspects of phylogenetic analysis. In the example above, flower color might be considered a good character if all species being examined have flowers of the same type, varying only in color. However, if the group contained species that did not ever flower, then the independence of the character flower color would be in question, because flower color would depend first on the presence or absence of flowers in general. Independence of characters is one of the main attractions of using molecular sequences for phylogenetic reconstruction. Since the early 1990s, use of sequence data from different genes has become so common in phylogenetic analysis that this methodology has its own term: molecular systematics.

CONVERGENT EVOLUTION

The evolution of similar features in organisms that do not share a recent common ancestor is termed convergence. Convergence is often the result of similar, selective environmental pressures acting on organisms in different parts of the world. The classic botanical example of convergent evolution involves three very different groups of flowering plantscacti, spurges, and milkweedsgrowing in similar desert environments in the New World, Asia, and Africa. The harsh desert environment favors adaptive characteristics that provide the capacity for water storage (such as large, fleshy stems) and protection from extremes of heat and dryness (reduced leaves or spines). Although members of these groups of plants resemble each other in appearance, they do not have a close common ancestor.

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phylogeny

phylogeny The evolutionary relationships within and between taxonomic levels, particularly the patterns of lines of descent, often branching, from one organism to another, i.e. the relationships of groups of organisms as reflected by their evolutionary history. See TAXONOMY.

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phylogeny

phylogeny Evolutionary relationships within and between taxonomic levels, particularly the patterns of lines of descent, often branching, from one organism to another (i.e. the relationships of groups of organisms as reflected by their evolutionary history).

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phylogeny

phylogeny Evolutionary relationships within and between taxonomic levels, particularly the patterns of lines of descent, often branching, from one organism to another (i.e. the relationships of groups of organisms as reflected by their evolutionary history).

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phylogeny

phylogeny Evolutionary relationships within and between taxonomic levels, particularly the patterns of lines of descent, often branching, from one organism to another (the relationships of groups of organisms as reflected by their evolutionary history).

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phylogeny

phylogeny The evolutionary history of an organism or group of related organisms. Compare ontogeny.

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phylogeny

phylogeny: see biogenetic law.

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